Wrecked nearly beyond repair, the USS Voyager hides in a class 9 nebula in the Delta Quadrant near the temporally-fluctuating Krenim-controlled space. The ventilation system, while still partially functional, has allowed nebular gas to flood one of the remaining decks. CaptainKathryn Janeway and EnsignHarry Kim don gas masks and enter the deck. They manage to fix the controls, preventing further damage, but the ventilation system is too damaged to eject the gas. Forced to repair the system, Janeway and Kim use up their respective air supplies. They struggle to keep from inhaling as they finish the job, but the gas enters their lungs and causes extensive damage. The Doctor treats Kim, but Janeway refuses to sit still long enough. The Doctor follows her to the bridge, trying to convince her to undergo treatment.

Janeway marches onto the remains of the bridge. Lieutenant jgB'Elanna Torres sits at the still somewhat functional conn station and reports on the status of the warp drive. One of the warp nacelles is still partially operable, but the other is beyond repair. Between violent fits of coughing, Janeway orders Torres to get the recoverable nacelle working again.

The Doctor and the captain argue. He implores her to stop working and rest for 48 hours, allowing her lungs time to heal. She refuses and demands an injection of trioxin to help her breathing. He objects, as trioxin is only a stopgap measure. Her lungs, he stresses, have been seriously damaged. He tries to invoke medical rank and force her acquiescence, but as captain, she issues a stern order to use the trioxin. Realizing further efforts will be futile, he reluctantly obeys. Despite coughing, she continues working.

Annorax sits at a table loaded with an impressive feast. He removes his uniform gloves and greets Chakotay. Chakotay asks about his crewmate, Tom Paris. Annorax responds that "no doubt he is making himself difficult". Chakotay asks what he expects, given their captivity for the last two months, in isolation, poked and prodded. Annorax, with dignified irritation, responds that he expects they would act with at least some level of dignity or restraint, of which Paris shows none.

Chakotay demands to know what Annorax wants from them. "At the moment, information" he politely replies. Paris enters and ascertains that Chakotay is unharmed. Annorax invites them to join him, describing the feast as a selection of delicacies found nowhere else in the galaxy.

The Starfleet officers accept. Annorax pours each a glass of an extremely rare vintage of Malkothian wine, noting that this bottle is the sole remaining component of the once-powerful Malkoth race. Everything else – their cities, culture – even the very species itself – never existed. In fact, every dish on the table has come from civilizations erased from time. When he informs Paris that he is "devouring the last remnants of the Alsuran Empire.", Paris stops eating immediately. Annorax recounts having collected artifacts from each of the hundreds of worlds he has erased, calling his weapon ship more than a weapon, but a "museum of lost histories."

His attention turns to Paris and Chakotay. Annorax says he's decided to spare Voyager, and instead, plans to try and alter the timeline and restore Voyager, thus achieving both their goals. They might even find themselves closer to the Alpha Quadrant. In order to make the necessary calculations, he needs information about their experiences in the Delta Quadrant, other races they encountered, and how their presence affected any species with whom they came into contact.

Paris does not believe him, bluntly asserting that the only reason Annorax has not destroyed Voyager is that he lost track of the ship and for the past two months, Janeway has successfully eluded him. Annorax threatens to destroy Voyager unless Paris and Chakotay cooperate. Paris derides the offer because no Starfleet serviceman would accept such a proposal – not at the cost of wiping out the entire existences of whole civilizations. He disgustedly rises to leave, expecting Chakotay to follow.

But Paris is shocked when Chakotay remains seated and orders him to wait. Chakotay asks Annorax if he can restore Voyager without harming anyone. Annorax says he can, but only with extreme difficulty. For his plan to succeed, Annorax needs their cooperation. Paris scoffs at the idea, refusing to obey Chakotay's order to return to his seat. Annorax has Obrist enter and take Paris to the guest quarters, encouraging him to think about it. Paris leaves without a word.

Annorax focuses on Chakotay, complimenting him on his ability to truly perceive time, as evidenced by his question about the possibility of restoring Voyager without harming anyone. He offers Chakotay the chance to work with him toward that end. Chakotay accepts and the two seal their agreement with a toast of Malkothian spirits.

Aboard Voyager, in the wreck of the mess hall, Janeway and the senior officers also toast, not with fine liquor, but with the "elixir of endurance", a concoction that Neelix has created using ration cubes, water, and Talaxian spices. It tastes horrible but, as Seven of Nine notes, taste is irrelevant. Janeway takes the opportunity to get situational updates from each of her officers. The Doctor has repaired an optronic error in his program. Kim also reports that the power grid should be up to 50% functionality in a few days.

But news from Torres frustrates her when she is told that it will take at least three weeks to fix the operational warp nacelle. Janeway curses figuratively as it appears that they will be stuck in this nebula forever when they should be out in open space, finding allies to fight against Annorax. She decides to leave the nebula the next morning. Seven objects that they should wait as long as possible to complete their repairs, but Janeway's mind is made up. Upon leaving the room, Tuvok notes that Seven should not challenge the captain in such a situation, even when her logic is flawed.

Aboard the Krenim weapon ship, Chakotay tries his hand at temporal incursion calculations. He has come up with an incursion in which erasing a comet that Voyager changed course to avoid eight months before will prevent her from ever entering Krenim space. Annorax lets him simulate it.

Chakotay attempts a simulated temporal incursion

But when he does, he is shocked when a totally unexpected simulated result occurs: eight thousand species are erased with the comet. Annorax, with a chuckle, explains that four billion years ago, fragments from the comet crashed into a planet, releasing hydrocarbons that caused the rise of several different plant species. These in turn fed other complex organisms. In time, several space-faring civilizations arose. By erasing the comet, he would cause these civilizations never to develop.

His smile fades. He explains that he too made this mistake. It was when he first oversaw the use of the weapon ship against a race called the Rilnar. The Rilnar had removed the Krenim Imperium as the dominant power of the region. Thus their erasure caused a causality paradox in which the Krenim stayed in power.

But it also caused an alternate timeline in which fifty million Krenim died of a plague within a year. This occurred because the Rilnar had introduced a critical antibody against the disease into Krenim physiology and their erasure took the antibody with it. He tells Chakotay that he has been seeking to correct that mistake by his incursions against species whose erasures his calculations show would undo this first incursion.

He again asks Chakotay for his help. Together, he asserts, they can restore the Krenim Imperium and Voyager and undo the damage he has caused. Chakotay tells him he, Chakotay, still has much to learn of temporal manipulation. Annorax takes him to see the heart of the weapon ship, the temporal core.

Day 180

A micro-meteoroid shower...

...hits Voyager

Voyager has left the nebula but a huge micro-meteoroid shower hits the crippled ship. Thousands of the microscopic rocks pelt her ruined hull, rapidly destroying what little is left. On the bridge, Janeway, amid the clanging and clattering of the meteoroid shower hitting the hull, asks Torres if engines are available yet, to get them out of the shower's way. Torres answers that they are not and Kim reminds Janeway their navigational deflector is nonfunctional. She orders Tuvok to divert emergency power to it, but is subsequently informed that there is "none available".

Janeway makes a decision. She rises from her command chair and announces she is heading for deflector control. Tuvok warns her that the area is far too hazardous, but she still goes. When she opens the door, she sees that there is a raging fire inside, so hot that she recoils against the opposite wall with a gasp. But she is determined to fix the deflector. Kim reports that the damage from the micro-meteoroid shower is growing rapidly.

Janeway orders Tuvok to prepare to engage the shields. She also tells him to inform The Doctor she will be coming back with severe burns. Tuvok objects, but she sternly repeats her order. Then, steeling herself, she charges into the inferno.

On the bridge, Kim reports that deflector shields have come on-line. Tuvok immediately raises them. The sound of the micro-meteoroids hitting the hull stops immediately. Tuvok hails Janeway, but she does not respond. Torres and Kim look blankly ahead in horror.

Janeway, unconscious and severely burned

Among the flames, Janeway lies unconscious on the floor. Half her face and one arm are seen to be severely burned.

Minutes later, Janeway, still unconscious, rests on a makeshift bed in what remains of the mess hall. The Doctor sighs deeply and reluctantly wakes her with a shot from a hypospray. Her eyes open and she asks him her condition. He informs her that she has suffered third-degree burns over 60% of her body. He was able to heal most of them but, not having a dermal regenerator, he could not heal the damage totally and her face and arms are scarred.

She rises, prepared to return to the bridge, but The Doctor stops her. This time, unlike the last, he is not about to let her have her way. With complete seriousness, he insists that she stay in the mess hall two days for observation. He has diagnosed the deadly risks she has been taking as signs of Traumatic Stress Syndrome. If she does not follow his instructions, he will relieve her of command. She warns him that if he tries it, she'll deactivate him which The Doctor simply takes as more proof of the syndrome. Janeway apologizes, but refuses to stay in the mess hall. The Doctor responds by using his authority as chief medical officer to officially relieve her of duty.

She asks him how he intends to have this enforced as there is no security staff except Tuvok, the brigs are both destroyed and the transverse force fields no longer work, thus she cannot be confined. He quietly reminds her that by disobeying his direct medical order she is now facing a court martial. She responds that if they do get back home, a court martial will be a small price to pay, given what she has endured and leaves the mess hall.

Janeway and Neelix, covered in sweat and grime, walk through Voyager's bombed-out corridors, assessing damage. Turning a corner, they find themselves in front of Chakotay's former quarters, now in ruins. Janeway whips out her tricorder and follows its signal inside the room, where she uncovers a still-intact pocket watch. Stunned, she murmurs, "You disobeyed orders." Neelix asks, "Captain?" and she replies, "Chakotay gave this to me five months ago – a birthday gift. I ordered him to..." but her voice trails off as she relives the memory. Struggling with her emotions, Janeway resolutely fastens the watch to her belt and her composure returns. She and Neelix continue on.

Paris plays a game with Obrist

On the weapon ship, Paris plays a Krenim board game with Obrist. To Obrist's amused astonishment, Paris wins convincingly, though he has never played the game before. Obrist reminisces that Paris' end-game sequence is the same one Obrist's brother favored. His face then falls. When Paris asks him what is wrong, he recalls sadly that he used to celebrate his brother's birthday, along with those of his parents and closest friend, until a hundred years ago when he realized that he was celebrating birthdays for people who were dead or, because of the temporal incursions, never even existed. Paris looks at him sympathetically and says, "I'm sorry."

Chakotay in his guest quarters, pores over a large PADD filled with temporal incursion calculations. Paris enters excitedly and reports he has vital information about the ship's defensive systems, information provided by Obrist, who, like many of the crew, has become discouraged and disillusioned with their seemingly endless mission. The ship, he tells Chakotay, depends on its temporal core for defense because it keeps the vessel out of the space-time continuum, making it immune to all conventional weapons. Due to its temporally fluctuating nature, its designers and builders paid little attention to conventional defenses and construction. As a result, its deflector shields are extremely weak. Paris wants to incite mutiny among the already disheartened crew and disable the temporal core, leaving the ship vulnerable to attack.

But Chakotay sternly forbids Paris from setting his ideas into motion. Instead, he says they will focus on Annorax's offer. Outraged, Paris becomes insubordinate, telling Chakotay that Annorax is flattering him with talk of his having an "instinct for time." Chakotay orders him to make no move against Annorax, insisting he is not a villain, but Paris will not agree telling Chakotay that he's hardly in a position to give orders any more. Chakotay warns Paris that if he refuses to maintain the chain of command, they can settle things 'the old fashioned way'. Following a tense moment between the two men, an alarm sounds.

They go to the bridge. Chakotay is shocked to find Annorax and crew proceeding with an incursion operation against the Ram Izad. Annorax explains that it occurred to him that their erasure would aid his mission. His calculations indicated a 52% restoration of the Krenim timeline. Horrified, Chakotay begs Annorax to stop, that he can achieve his goals in other ways. Paris, in a low, angry voice, mocks Chakotay's decision to work with Annorax.

Absorbed in the impending incursion, Annorax ignores Chakotay's desperate pleas and commands, "Prepare for total erasure", and seconds later, "Fire". Stunned, Paris and Chakotay watch as the weapon's temporal laser drills onto the Ram Izad homeworld. A temporal shock wave spreads out over the planet, then beyond, eradicating the species from existence. Obrist reports the results as the sensors track the wave. Annorax orders him to continue, then retires to his quarters. Paris, fuming, tells Chakotay under his breath that he will deal with "this maniac" if Chakotay will not.

Chakotay enters Annorax's quarters and heatedly insists he did not need to fire on that planet. Annorax, indifferent to suffering other than his own, points out that he's altering history on a massive scale, that the destinies of countless star systems are in his hands; one species is insignificant. Unswayed, Chakotay argues, "You're trying to rationalize genocide. One species is significant. A single life is significant." Annorax's face falls into the same guilty expression it had when he first told Chakotay why he was doing this. It was so easy the first time, he recalls. In the blink of an eye, he'd changed history itself. But on his next incursion, when he changed history a second time, he lost "more than you can imagine."

"The colony on Kyana Prime", says Chakotay, who explains he's been studying Annorax's previous incursions and no matter how close he came to restoring the glory of the Imperium, one component was always missing... the colony on Kyana Prime. Annorax admits this is true and tells Chakotay why he is obsessed with its restoration – his beloved wife was on Kyana Prime. Her erasure took her away, along with his future, his children and grandchildren. He picks up the pyramid containing the lock of hair and tells Chakotay that it is his wife's hair. He asserts that time itself is against him, keeping him from her in angry retaliation for his arrogant manipulation of it.

Obrist enters and reports to Annorax that he was correct and a 52% restoration of the Imperium was achieved. As usual, Annorax asks him about Kyana Prime. Obrist fails to completely contain his exasperated anger and he states again, that it has not and questions Annorax's continued manipulation of the timeline. Annorax notes his feelings on changing the timelines and dismisses him. He then tells Chakotay that Chakotay's calculations are promising, but need more work. While he is working on them, he will continue his mission. Chakotay begins to angrily rebuke him, telling him he does not have the right to do what he is doing, but Annorax responds that he indeed has the right to fight for what is his and only time itself can judge him, not Chakotay.

In Chakotay's guest quarters, Paris fumes as he asserts that Annorax is insane, after Chakotay has informed him of what he said about time having it in for him. Chakotay finally agrees with Paris that Annorax must be stopped, not worked with. Paris informs him that he believes that Obrist will help them get a message to Voyager, informing Janeway of the ship's location. Obrist will also help him sabotage the temporal core, taking it offline so that the ship will be vulnerable against conventional attacks. Chakotay gives him the go-ahead to proceed with his planned mutiny.

Day 226

Voyager leads a small fleet against the temporal weapon ship

"Captain's log, stardate 51682.2. I've forged a coalition with the Nihydron and the Mawasi. Together, we're preparing to attack the weapon ship."

Voyager is seen in formation with four other ships from the coalition.

Janeway addresses her senior staff on the wrecked bridge

Janeway addresses her officers on the bridge which is now all but destroyed. Almost all of the lights are out, the displays are dark and cracked, consoles are covered in dust and the room is black and marred with twisted debris. The only functioning area is the command section.

She informs them that she has received an authenticated message from Paris, giving her the location of the weapon ship, as well as the location of its temporal core. Paris has promised to try and take its temporal core offline, leaving the ship vulnerable to conventional weapons. Voyager and her allied ships will then disable the weapon ship and retrieve Paris and Chakotay.

She then issues instructions to the officers. Kim and Torres will go to the lead Nihydron ship while Tuvok, Seven, Neelix, and The Doctor will go to the lead Mawasi ship. All ships are to be outfitted with temporal shielding. She will remain aboard and pilot Voyager. Torres questions Janeway's decision, claiming Voyager has barely enough to reach the battle, let alone fight one, but Janeway believes that the six photon torpedoes and temporal shields that the ship has left will be enough to hold her own. Furthermore, she believes that the captain must go down with the ship.

The crew disembarks, except for Tuvok. Janeway tells him that Voyager needs her, but Tuvok argues how illogical her decision is and is puzzled by the Human predilection to bond with inanimate objects, as Janeway has done with Voyager. She tells him that the ship has been their home and she feels as close to it as any member of the crew. She elaborates that the ship has carried them, even nurtured them, and now needs one of them. Tuvok respects Janeway's decision and gives her the traditional Vulcan salute, intoning "Live long and prosper" to his captain and dear friend. Janeway reciprocates and embraces Tuvok in a hug, which the Vulcan returns, deeply affecting Janeway as she realizes what he has done. Alone on the bridge, Janeway checks the watch that Chakotay gave her and with a quick glance at the empty first officer's chair and around the silent bridge, the captain assumes her station.

Voyager and the other ships reach the Krenim weapon ship. Aboard the ship, Chakotay and Paris put their plan into action. They have succeeded in getting Obrist to support their mutiny. On the bridge, Obrist informs Annorax of the approach of the attacking vessels. At first he is unconcerned, since the ship is immune to conventional weapons. Chakotay makes him pause by telling him that Captain Janeway would not be attacking unless she knew she could do damage somehow.

Further, Chakotay reminds him of Voyager's temporal shields and tells him Janeway has probably given the technology to the other ships. Also, he continues, she may have also passed it onto the homeworlds in the region and warned them about him and his ship. This is totally unacceptable to him, of course as he cannot have potential targets protected from his weapon. True, the weapon has proven able to degrade Voyager's temporal shields, but what if those who receive the technology are able to improve it so that that no longer happens? He orders Obrist to bring the weapon online and prepare for multiple incursions against the attacking ships.

Obrist does so; however, he also secretly transmits information to Paris in his guest quarters about the temporal core. Paris begins attempting to shut it down. Aboard Voyager, Janeway orders the attack commenced. Two Nihydron ships go in and perform a strafing attack.

But, try as he might, Paris fails to take the temporal core offline. The Nihydron weapons do not harm the weapon ship. On Annorax's order, the temporal incursion beam is fired on them. Its power almost immediately overwhelms their temporal shields and they vanish, erased from history. Janeway orders the fleet to engage in evasive maneuvers. She verbally wills Paris to succeed.

Paris fails, but Obrist, on seeing that Paris is having no luck, takes over for him. Annorax orders him to target the other ships. He does not, instead, exchanging a look with Chakotay. Annorax repeats his order. Obrist works the controls, but instead of the beam attacking another ship, the weapon ship shudders and alarms go off. Annorax, shocked, sees that he has been betrayed; Obrist has taken the temporal core offline. Obrist apologizes to him sadly, but firmly and states that this must end now. He works the console again and beams Chakotay and Paris to a Mawasi ship. Annorax angrily rises from his command chair, rushes to the console and pushes him away. He notes with alarm that they are phasing back into the space-time continuum. They are now vulnerable to the attacking ships' weapons.

He orders reconfiguration to conventional weapons. Another officer obeys. He orders firing at will and bursts of energy begin flashing from cannons on the ship's hull like Gatling guns.

Janeway watches the weapon ship through a breach in the forward bulkhead

As limited as the ship's conventional weapons are, however, they are still powerful enough to disable most of the attacking ships, one of which loses helm control and collides into Voyager's primary hull. A huge chunk of the saucer section is destroyed with the majority of the rest of the section burning in space. Janeway, who was at the conn console, is thrown violently out of the seat by the collision. Sparks fly and smoke rises in the room. Janeway crawls to her command seat. What she sees ahead of her on sitting down visibly stuns her, the entire forward bulkhead is gone. Nothing now separates Janeway from open space but an emergency force field, which fritzes in and out with the power remaining. She sees the weapon ship straight ahead. Aboard it, Annorax orders fire concentrated on Voyager.

Janeway hails the other ships and instructs them to take their temporal shields offline and does the same to Voyager. Tuvok objects that they will no longer be protected from the weapon ship's temporal incursion beam, but removing their protection is just what she wants. She tells Tuvok and the other ship commanders her plan to ram Voyager into the ship where the temporal core is located. This, she hopes, will destroy the ship and reverse all the damage it has ever caused.

Janeway's kamikaze attack on the weapon ship

As she stares forward at the weapon ship, teeth gritted, she sets course. Just before the collision, she grits her teeth and says "Time's up." Voyager plows into the weapon ship in a huge explosion of flame and debris, utterly destroying itself. The weapon ship shakes violently. Sparks fly on the bridge, Annorax and the bridge officers are knocked off their feet. Annorax notes with horror the destabilization of the temporal core and the imminent temporal incursion that will occur within the ship.

He rises and hurries to his quarters just in time to see the pyramid containing the lock of his wife's hair fall and shatter. He watches this with horror but his expression changes to one of wonder as the hair vanishes. He looks at the spot where it was, as it suddenly dawns on him what is about to happen...

The weapon ship explodes and then is engulfed by a temporal shock wave, erasing itself from history.

Day 1

"Captain's log, stardate 51252.3. The past couple of weeks have been uneventful but we've made excellent progress on the new astrometrics lab."

Voyager, undamaged, continues on her journey home. On the bridge are Captain Janeway, Chakotay and the duty officers, clean and relaxed, along with Seven of Nine.

The "Year of Hell" never happened...

...and will not happen...

A Krenim warship approaches and hails. Janeway orders an on-screen answer. It is the Krenim commandant. His demeanor, though curt, is not hostile and his ship does not attack Voyager. He informs Janeway that they have entered Krenim space and instructs her to identify herself and her ship. When she does so, he informs her that the region is in dispute, suggesting she avoid it.

Janeway thanks him. He wishes them a good journey and cuts the communication. He and his race remain completely unknown to Voyager's crew. Janeway and Chakotay decide to have a commissioning ceremony for the astrometrics lab, complete with fine liquor: a bottle of Saint-Émilion, 2370. Janeway jokes to Chakotay that she heard this was "a good year".

...or will it?

Restored to Kyana Prime in the 2170s, Annorax sits at a desk in his home, working on a large PADD. His wife comes to him and asks him to join her for breakfast and he tells her he will do so in a little while but he still has "a few more calculations". She lovingly chides him that he always says that and reaches her hand out to him, sweet-talking him into putting the PADD down and spending the day with her. He rises and takes her hand with a smile and they leave together.

The work he was doing on the PADD is seen... it is temporal incursion calculations.

"It's your body; who am I to judge? I'm only the chief medical officer; what do I know?"

- The Doctor, to Captain Janeway

(Speaking about Paris) "I've never seen such an intransigent young man."
"You've had us in isolation for two months. We've been scanned, poked, and prodded. How do you expect us to act?"
"With some degree of dignity and restraint. Your crewmate has none."

- Annorax and Chakotay

"This vessel is more than a weapon. It's a museum of lost histories."

- Annorax

"It is offensive. Fortunately, taste is irrelevant."

- Seven of Nine, regarding Neelix's "Elixir of Endurance"

"Remember this guideline: the captain is always right."
"Even when you know that her logic is flawed?"
(Pauses with uncertainty) "Perhaps."

- Tuvok and Seven of Nine

"You've been at this for 200 years, Annorax. What makes you think you're ever going to succeed?"
"What makes you think Voyager will ever reach Earth? The odds against you are astronomical. Yet you keep trying."

- Chakotay and Annorax

"What are you going to do, take away my holodeck privileges? "
"Either we maintain our command structure, or else we settle this the old fashioned way."

- Paris and Chakotay, after Paris wants to start a mutiny

"Have you seen enough yet, Chakotay? If you won't do something about this maniac, I will".

- Paris, to Chakotay after Annorax has erased the Ram Izad from time

"If that little display didn't convince you, I don't know what will. He's insane!"
"No, he's not. Wounded, maybe. But I can still reach him; convince him to stop."
"Not from what you've told me. This guy thinks that time has a personal grudge against him! That's called paranoia, Chakotay; with a hint of megalomania."
"You don't know what he's been through."
"He's lost his family. Okay, that's a terrible thing. But so has everyone else on this ship. AND, FRANKLY, SO HAVE WE!"

- Paris and Chakotay, discussing Annorax privately after watching him erase a civilization from history

"Tuvok, I can hear your objections already. I am not leaving."
"Given Voyager's damaged state, the probability of your surviving an armed conflict … is marginal."
"Oh, I know the odds. But I have to stay. Voyager's done too much for us."
"Curious. I have never understood the Human compulsion to emotionally bond with inanimate objects. This vessel has done nothing. It is an assemblage of bulkheads, conduits, tritanium – nothing more."
"Oh, you're wrong. It's much more than that. This ship has been our home. It's kept us together. It's been part of our family. As illogical as this might sound, I feel as close to Voyager as I do to any other member of my crew. It's carried us, Tuvok. Even nurtured us. And right now, it needs one of us."
"I respect your decision. Live long and prosper, captain."
"Same to you, … old friend."

- Janeway and Tuvok

"Target Voyager. Put Janeway out of her misery."

- Annorax

"If that ship is destroyed, all of history might be restored. And this is one year I'd like to forget."

- Janeway

"Time's up!"

- Janeway's last words before ramming Voyager into the weapon ship

"It's a beautiful day. Spend it with me?"
"I suppose I can make the time."

Originally, episode co-writer Brannon Braga did not want the "Year of Hell" story arc to end in a second part such as this, but with a fourth episode. He later remembered, "I was pushing to make it four parts, but ended up with two." (Cinefantastique, Vol. 30, No. 9/10, p. 108)

Brannon Braga and Joe Menosky temporarily struggled with writing the majority of this episode. Menosky related, "We've got the bad guy, the weapon ship, the first episode, and the ship wrecked. We're doing this over the course of a year, and we've got those [day-setting] subtitles. We've planned out an episode and about a quarter, and we had no idea how to fill the rest of that second part. We had run out of story. I think we were totally stuck a week or two weeks." (Cinefantastique, Vol. 30, No. 9/10, p. 108)

Following this period of uncertainty, Brannon Braga came up with the solution of basing the rest of the story (especially the character of Annorax) on Jules Verne's Twenty Thousand Leagues Under the Sea (and especially the persona of Captain Nemo). Joe Menosky recollected, "Brannon came in one morning and said, 'It's Twenty Thousand Leagues Under the Sea. This guy [Annorax] is Nemo.' That was all it took. We sat down, watched Twenty Thousand Leagues. The character of Nemo was just awesome, because he's a bad guy but he's also a hero. He's evil, but he's also tortured, and all of that informed the character. All we had was a guy who was changing the timeline to benefit his race. But as soon as you had Nemo [...] you had a guy who was trying to not just restore the timeline, but to bring back his wife who was lost to him through his own arrogance. That gave us the whole second episode." (Cinefantastique, Vol. 30, No. 9/10, p. 108) For his part, Braga described Annorax as "a villain that we modeled after Captain Nemo." (Star Trek Monthly issue 34, p. 15) An in-joke that plays on this link between Annorax and Nemo is when Tom Paris, in this episode, refers to Annorax as "Captain Nemo" while conversing with Chakotay.

Despite the viability of this influence, the writers were still not entirely certain about how to draw the episode to a conclusion. "We had at least half a dozen different endings, and reshot endings," Joe Menosky recalled. "Brannon wanted to keep the ship wrecked for the entire season, and he didn't want to end with a reset. The studio [namely, Paramount Pictures] didn't want to do that. [Executive producer] Rick Berman didn't want to do that. So we didn't do that. I wanted at least a couple of people to know what had happened. We actually wrote this ending even though we didn't shoot it, where time is reset, the weapon is gone; we know what has happened to us through some complication I can't even remember. When we meet up with the next Krenim, Chakotay asks offhand, 'Have you got a colony called Kyana Prime?' And the guy says, 'Sorry, I don't know what you're talking about.' The idea was that time had in fact in some ways punished Annorax. Everything was reset except that. That was denied him, so it was this great, final, tragic moment. That was written and never shot because Rick said it was too complicated, and he was right. I can't even remember the tortured reasoning we had so that some of us could remember. Rick said, 'Just plow Voyager into the weapon ship, and reset the timeline, and nobody remembers.' That was the simplest solution." At the time, however, Menosky regretted the ending that was chosen. "I wasn't completely satisfied with it," he remembered. (Cinefantastique, Vol. 30, No. 9/10, p. 109)

Joe Menosky did, on the other hand, enjoy writing some of Annorax's dialogue, particularly when it is made clear that the character is personifying time. Menosky reminisced, "I loved Annorax's speeches in 'Part II' [....] That stuff was really fun to write." (Cinefantastique, Vol. 30, No. 9/10, p. 108)

The name "Annorax" seems to have been created intentionally to fit with the theme of time that is associated with that character, the word "anno" being Latin for "year." However, in A Vision of the Future - Star Trek: Voyager, author Stephen Edward Poe suggests that producers created the name of Annorax as a not-so-subtle dig at the more obsessive Trekkies (Anoraks). It may also have been an anagram for "Aronnax", a fictional professor who serves as the narrator of Twenty Thousand Leagues Under the Sea, a possibility supposed by the Star Trek Encyclopedia (3rd ed., p. 581).

Although Chakotay and Tom Paris find Annorax's methods debatable in this episode, Joe Menosky's interpretation of the character favored Paris' opinion of Annorax. "This guy was personalizing time. His paranoia, and his sense of guilt and megalomania were crashing in on him," Menosky stated, "to the point where he thought time itself was after him to punish him for his arrogance." (Cinefantastique, Vol. 30, No. 9/10, p. 108)

Executive producer Jeri Taylor found Annorax to be a notable character. "He's a very three-dimensional villain," she observed, "and in part two you really see him come to the surface. There's a lot going on with Chakotay and him." (Star Trek Monthly issue 36, p. 13)

Annorax actor Kurtwood Smith enjoyed appearing in this episode and the previous one. He remarked, "I liked Annorax. He was Captain Nemo, though not in terms of his behavior or personality. Nemo wandered through the oceans, while this guy wandered through space and time. I empathized with him [....] I had a good time with Annorax, and I got the girl at the end. If you know my career, you know that almost never happens." (The Official Star Trek: Voyager Magazine, issue #18)

Kurtwood Smith especially enjoyed working with a particular pair of Voyager's main cast members in this episode. He commented, "I actually didn't work with the regulars in the first show [of the "Year of Hell" two-parter], but I got to work with Robert Beltran and Robert Duncan McNeill in the second. They're all good people." (The Official Star Trek: Voyager Magazine, issue #18)

Tuvok actor Tim Russ observed that this episode's two-parter gives an insight into an alternate version of the relationship between Tuvok and Seven of Nine. "You see [...] what direction it could have gone into," noted Russ. (Cinefantastique, Vol. 30, No. 9/10, p. 101)

This is the first episode of Star Trek: Voyager to be directed by Mike Vejar, who went on to direct twelve subsequent installments of the series. Joe Menosky was extremely pleased with Vejar's work on this episode and said of both parts of the "Year of the Hell" two-parter (despite each of the two episodes having been helmed by a different director) that they "were amazingly well directed." (Cinefantastique, Vol. 30, No. 9/10, p. 108)

CGI Effects Director Ron Thornton thoroughly enjoyed the opportunity that Foundation Imaging was given to blow Voyager up for this episode. He noted, "Getting the chance to destroy Voyager at the end was very cool!" (The Official Star Trek: Voyager Magazine, issue #16) Visual effects supervisor Mitch Suskin and coordinator Arthur J. Codron also worked on this episode, in a changeover of supervisor and coordinator from the first half of the "Year of Hell" two-parter, and the look of this episode (as well as the previous one) were added to in the compositing bay, by animation effects artist Greg Rainoff. (Cinefantastique, Vol. 30, No. 9/10, pp. 108-109)

The soundtrack of this episode's two-parter includes some rare instances of melodic content, chordal arrangements having been usual since the first season of TNG. During the recording of the score for Star Trek: Voyager's fourth season finale, "Hope and Fear", composer Dennis McCarthy reckoned, "I think the last time I wrote a melodic piece was in 'Year of Hell'." (Star Trek: Action!, p. 91)

This episode achieved a Nielsen rating of 5.2 million homes, and an 8% share. [3]

Upon its first broadcast in Great Britain (on the BBC), this episode was shown edited together with the first half of its two-parter, forming a feature-length television movie, although it was not intended to be viewed that way. (Delta Quadrant, p. 207)

Ultimately, Brannon Braga believed that certain chances he and Joe Menosky had taken while writing this episode's two-parter had paid off. Shortly after the duology first aired in the US, Braga remarked, "We took some big chances with that show, and I think it's really interesting." Braga thought that a good example of the two-parter's quality was the destruction of Voyager in this episode's conclusion. "It's just filled with that kind of sweeping drama," he enthused. (Star Trek Monthly issue 34, p. 15) Braga also counted this episode's two-parter as a highlight of the fourth season (along with "The Killing Game" and "The Killing Game, Part II" as well as "Prey"), and opined that – in common with the two-parter "The Killing Game" – this episode's duology involved "high concept stories with an epic sweep, with big cinematic action sequences, and all of the characters [having] something fun to do." (Star Trek Monthly issue 44, p. 12) An element of the two-parter's development that Braga felt was "unfortunate" was that he and Menosky had chosen to make Tuvok blind. Braga explained that his reasoning for disliking this element of the plot was "because of the Geordi La Forge connection," referencing the fact that Tim Russ had been temporarily considered to play the character of Geordi La Forge on TNG. (Cinefantastique, Vol. 30, No. 9/10, p. 100)

Joe Menosky thought that, due to the caliber of actor he believed Kurtwood Smith to be, the "Year of Hell" two-parter "worked really, really well." In common with Brannon Braga, Menosky was ultimately satisfied with this episode's ending, despite having had initial feelings to the contrary. He opined, "It got us a great climax, which is plowing the ship into the weapon, and in some ways took the arc of destroying the ship to its ultimate conclusion, and a very satisfying conclusion." (Cinefantastique, Vol. 30, No. 9/10, pp. 108 & 109)

Jeri Taylor was also highly satisfied, ultimately, with the "Year of Hell" two-parter. Citing it as a highlight of Star Trek: Voyager's fourth season, Taylor counted it as an example of "some of our more epic episodes [that] had everything going for them." (Star Trek Monthly issue 40, pp. 14-15) Taylor further enthused about the two-parter, "It had a lot of action, a gigantic adventure, personal stakes, an intriguing villain and a very science fiction-based premise. Those are the things we love to get." (Star Trek Monthly issue 40, p. 15)

This episode's ending was controversial among fans. "Obviously we angered a lot of people with the ending," Joe Menosky admitted. Remembering a particular manifestation of this fan response, he stated, "I got one of the greatest little pieces of fan mail I've ever gotten, from a fan who said, 'Annorax is the best Trek villain in all of Trek history.' Then he went on to say in the same letter, 'I'm sorry to say that I'm not going to be watching Voyager anymore,' because he was so incensed about the ending, about the reset button." Of course, not all fan response to the episode's conclusion was negative. "I got a really interesting fan letter from someone who just loved the ending," Menosky also related. "Her take on it was that Janeway made this big sacrifice, and everything was reset, and then both of them were subtly changed, both the villain and the hero, both Janeway and Annorax, even though neither of them knew and was aware of that timeline. Somehow there was a hint that something positive had changed. Janeway was just a little less arrogant, for example, when the Krenim came on the viewscreen [....] For this fan, there seemed to be this interesting sense of a positive and a humanizing effect that the adventure had on both Janeway and Annorax." (Cinefantastique, Vol. 30, No. 9/10, p. 109)

Star Trek author Kirsten Beyer disliked the conclusion of this episode. "It was [a] fabulous episode right up until the end [....] The whole thing just made me sad," Beyer remarked, "because the writers did it to themselves. They had no business going as far as they did if they didn’t have a better resolution in their pocket." [4]

This episode was nominated for an Emmy Award for Outstanding Special Visual Effects for a Series.

After leaving Star Trek, Ronald D. Moore used this episode as an example of how he believed Star Trek: Voyager should have proceeded all along but also implied that he was not fond of the way in which this episode ends. [5]

Following his appearances in this episode and the previous one, Kurtwood Smith considered the possibility of returning to Voyager as Annorax. "As 'Year of Hell Part II' ended," the actor said, "you saw Annorax with his wife, but the camera also moves in to show you that he's designing something. If it's that ship and he hasn't learned his lesson–who knows?–he could be back again. If they come up with a story as good as 'Year of Hell,' count me in. I would love to do it." (The Official Star Trek: Voyager Magazine, issue #18) However, the writers were – or, at least, Joe Menosky was – admittedly unsure what would become of Annorax, following this episode's final scene. "Does he give up work, spend more time with his family, and become more humanized? I don't know," Menosky conceded. (Cinefantastique, Vol. 30, No. 9/10, p. 109) Perhaps as a result of this uncertainty, this episode's two-parter constitutes the only Star Trek production in which the character of Annorax features.

As well as referring to Annorax as "Captain Nemo" here, Tom Paris also implies a comparison between Annorax and Captain Bligh, referencing the historical British Vice Admiral William Bligh and implying a reference to a well known mutiny on the HMS Bounty – a seafaring craft that was under the command of Bligh when the takeover occurred.

This episode is the only one in the seven-year run of Voyager wherein Janeway is relieved of command (albeit momentarily) by the EMH, on the grounds that she is suffering from Traumatic Stress Syndrome.

This episode is the second to feature the complete destruction of Voyager, and is the fifth of many times Janeway "dies" in the series. On this occasion, she dies along with the destruction of Voyager.

This is the second consecutive episode to feature no scenes in Voyager's engineering and sickbay departments.